Complex diseases, such as diabetes, Alzheimer's, and others are controlled by a large number of potentially interacting genetic and environmental factors. If the genetic loci contributing to variation in disease risk can be resolved, novel therapeutic regimens, and genetic tests that facilitate tailored disease treatments may be suggested. However, we are far from identifying the catalog of causative sites that influence variation in susceptibility to any complex disease, or indeed variation in any quantitative trait. As a byproduct, we remain ignorant of the evolutionary forces that shape segregating variation underlying complex disease. It may be that relevant polymorphisms are continually created by mutation, but are so strongly deleterious that they are rapidly eliminated from the population before they attain high frequency. Alternatively, polymorphisms may be actively maintained at intermediate-frequency by various forms of balancing selection. For instance, alternate alleles may be favored under different environmental conditions, leading to the maintenance of multiple alleles in a population. To gain insight into the pattern of genetic variation for complex traits, we must understand the relative roles of rare deleterious mutations and common selectively-maintained polymorphisms. Experimental tests can best be carried out in model genetic systems, employing traits that are subject to selection, dissecting trait variation both in large semi-natural laboratory panels and in natural populations. The trait we focus on here, the posterior lobe, is a male-limited Drosophila genital trait that shows striking morphological differentiation among closely-related species. Rapid evolution is a general feature of male genitalia in animals, and the posterior lobe also exhibits significant within-species variation. The primary goal of this proposal is to characterize the genetic factors that contribute to morphological variation within the model organism D. melanogaster. To achieve this we will utilize a novel genetic mapping approach in a replicated study across two large, independent mapping panels. The method we employ is unique in providing an estimate of the population frequency of mapped QTL, and thus can distinguish between theoretical models that seek to explain the maintenance of variation. In addition, our framework offers a streamlined approach to move from QTL to the precise nucleotides involved. We will validate these sites, and identify replicable causative variants by follow-up association tests in multiple wild-derived populations. Finally, to elucidate the processes that led to the dramatic divergence in posterior lobe morphology among species, we will compare the genetic architecture of intraspecific trait variation to that seen in between-species crosses. Our use of thousands of recombinant hybrid individuals will provide the high resolution data required to articulate this relationship.